update notebooks

pughlab · Oct 12, 2021 · d8420d1 · d8420d1
1 parent 599a82e
commit d8420d1
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Showing 7 changed files with 633 additions and 213 deletions.
diff --git a/notebooks/02_Master_manifest.ipynb b/notebooks/02_Master_manifest.ipynb
@@ -1818,6 +1818,97 @@
     "DKFZ_manifest$cohort[grepl(\"ETMR\", DKFZ_manifest$cohort)] <- \"ET\""
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 80,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style>\n",
+       ".list-inline {list-style: none; margin:0; padding: 0}\n",
+       ".list-inline>li {display: inline-block}\n",
+       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
+       "</style>\n",
+       "<ol class=list-inline><li>'HGGother_WT'</li><li>'HGGother_IDH'</li><li>'HGG_K27M_K27M'</li><li>'HGG_K27M_K27M'</li><li>'HGGother_IDH'</li><li>'HGG_K27M_K27M'</li><li>'HGG_K27M_K27M'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_G34R'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGG_K27M_K27M'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_WT'</li><li>'HGGother_IDH'</li><li>'HGGother_G34R'</li><li>'HGG_K27M_K27M'</li><li>'HGG_K27M_K27M'</li><li>'HGGother_IDH'</li></ol>\n"
+      ],
+      "text/latex": [
+       "\\begin{enumerate*}\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_IDH'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGGother\\_IDH'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_G34R'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_WT'\n",
+       "\\item 'HGGother\\_IDH'\n",
+       "\\item 'HGGother\\_G34R'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGG\\_K27M\\_K27M'\n",
+       "\\item 'HGGother\\_IDH'\n",
+       "\\end{enumerate*}\n"
+      ],
+      "text/markdown": [
+       "1. 'HGGother_WT'\n",
+       "2. 'HGGother_IDH'\n",
+       "3. 'HGG_K27M_K27M'\n",
+       "4. 'HGG_K27M_K27M'\n",
+       "5. 'HGGother_IDH'\n",
+       "6. 'HGG_K27M_K27M'\n",
+       "7. 'HGG_K27M_K27M'\n",
+       "8. 'HGGother_WT'\n",
+       "9. 'HGGother_WT'\n",
+       "10. 'HGGother_WT'\n",
+       "11. 'HGGother_WT'\n",
+       "12. 'HGGother_WT'\n",
+       "13. 'HGGother_G34R'\n",
+       "14. 'HGGother_WT'\n",
+       "15. 'HGGother_WT'\n",
+       "16. 'HGG_K27M_K27M'\n",
+       "17. 'HGGother_WT'\n",
+       "18. 'HGGother_WT'\n",
+       "19. 'HGGother_WT'\n",
+       "20. 'HGGother_WT'\n",
+       "21. 'HGGother_IDH'\n",
+       "22. 'HGGother_G34R'\n",
+       "23. 'HGG_K27M_K27M'\n",
+       "24. 'HGG_K27M_K27M'\n",
+       "25. 'HGGother_IDH'\n",
+       "\n",
+       "\n"
+      ],
+      "text/plain": [
+       " [1] \"HGGother_WT\"   \"HGGother_IDH\"  \"HGG_K27M_K27M\" \"HGG_K27M_K27M\"\n",
+       " [5] \"HGGother_IDH\"  \"HGG_K27M_K27M\" \"HGG_K27M_K27M\" \"HGGother_WT\"  \n",
+       " [9] \"HGGother_WT\"   \"HGGother_WT\"   \"HGGother_WT\"   \"HGGother_WT\"  \n",
+       "[13] \"HGGother_G34R\" \"HGGother_WT\"   \"HGGother_WT\"   \"HGG_K27M_K27M\"\n",
+       "[17] \"HGGother_WT\"   \"HGGother_WT\"   \"HGGother_WT\"   \"HGGother_WT\"  \n",
+       "[21] \"HGGother_IDH\"  \"HGGother_G34R\" \"HGG_K27M_K27M\" \"HGG_K27M_K27M\"\n",
+       "[25] \"HGGother_IDH\" "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "DKFZ_manifest$disease_type[ DKFZ_manifest$cohort == \"pedHGG\"]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -2876,7 +2967,7 @@
     "height": "calc(100% - 180px)",
     "left": "10px",
     "top": "150px",
-    "width": "249px"
+    "width": "248.991px"
    },
    "toc_section_display": true,
    "toc_window_display": true

diff --git a/notebooks/05_Cohort_cleanup.ipynb b/notebooks/05_Cohort_cleanup.ipynb
@@ -680,7 +680,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 41,
    "metadata": {},
    "outputs": [],
    "source": [